Hello
Here are a few suggestion you can try that may speed up your code.
Instead of GetSubstructMatches, you can use the list of neighbours of each
atom. Here is something that may work, it creates an iterator that will
return all the atoms for bond angles. I did not test it, however it may
give
On 09/14/2016 02:23 PM, Dimitri Maziuk wrote:
> lbl=mol.GetAtomWithIdx(s[0]).GetSymbol() + str(s[0]+1)
> print label, ":", s[1]
^^^
Should be lbl
--
Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
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I don't know if this fits in the Getting Started, or Cookbook, or if
TPTB decide to wikify the docs and it should go there, but anyway, here
goes. With thanks to everyone responsible, of course.
It does need corrections/clarifications.
-
# MOL/SDF FindChiralCenters
Dear Greg,
I found my mistake I need the bond angle not the torsion.
I add this function for that...
from numpy import (array, dot, arccos, clip,zeros,degrees)
from numpy.linalg import norm
def cangle(v1,v2):
c=dot(v1,v2)/norm(v1)/norm(v2) # -> cosine of the angle
return arccos(clip
Hi Greg,
here the first code prototype of the article mappiing in rdkit: for the moment
I have some issues with angle the rest start to be ok
Can you look at it and see if my interpretation is ok ?
BR,
Guillaume
---
import sys
import re
from rdkit import Chem
from rdkit.Chem
On Wed, Sep 14, 2016 at 4:16 AM, Guillaume GODIN <
guillaume.go...@firmenich.com> wrote:
> Your solution is perfect!
>
>
> glad it worked
> I am currently implementing this article "http://www.mdpi.com/1420-
> 3049/20/10/18279" using RDKit.
>
>
Interesting, I hadn't seen that one.
> It's now
Hi Guillaume,
Greg's solution is great for intra-molecular H-Bonds. If you want to
achieve inter-molecular ones then it's a bit more complicated. I did such
implementation in my package ODDT [https://github.com/oddt/oddt], which
also uses RDKit. You can find the hbond function in interactions modu
Dear Greg,
Your solution is perfect!
BTW, I was also looking for the intramolecular H-H distances, and your function
can be a modify to do this too:
def
findintramolecularHH(m,confId=-1,possiblePartners='[#1][*]',possibleHs='[#1]',distThresh=2.5):
conf = m.GetConformer(confId)
partn
Hi Guillaume,
On Tue, Sep 13, 2016 at 10:12 PM, Guillaume GODIN <
guillaume.go...@firmenich.com> wrote:
> 1 Does 3D coordinates of a conformer is in Angstroms ?
>
> If you read the conformer from a file, for example a mol file, then the 3D
coordinates are in whatever units they were in in that fi
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